Enzymes employ metal ions (e.g. Mg, Cr, Mn, Fe, Co, Ni, Cu, Zn) for catalysing certain reactions.
Let's consider planting a seed. Where will it obtain these metal ions from? Just from water?
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Many ions are absorbed by the plants via the action of bacterias. Fe or B for example require chelating action from microbes. P and S need to be oxidised to enter the plant as well. Source: Le sol, la Terre et les Champs - http://www.sangdelaterre.fr/index_135_151.html
The question is a little bit dubious, because when the OP says "seed" we tend to think about the seed before germination.
If you are talking strictly about the seed, it doesn't absorb from anywhere: the seed normally contains inside it all the macro and micro nutrients necessary for the first days after germination.
Of course, after a while, the growing sporophyte will need more macro and micro nutrients. These nutrients are already dissolved in soil (or in the water, for the aquatic plants), as non-charged compounds or as ions, and are absorbed mainly by the root system (whose cells have several different channels for absorbing them).
When the soil is poor in one of these nutrients, very interesting evolutive strategies may develop to obtain nutrients, as in the "carnivorous" plants. Note: the nutrients are classified in macro and micro not by the size or the weight of the atom, as the name may imply, but by the amount needed.